Abstract

Background

More and more completely sequenced fungal genomes are becoming available and many
more sequencing projects are in progress. This deluge of data should improve our knowledge
of the various primary and secondary metabolisms of Fungi, including their synthesis
of useful compounds such as antibiotics or toxic molecules such as mycotoxins. Functional
annotation of many fungal genomes is imperfect, especially of genes encoding enzymes,
so we need dedicated tools to analyze their metabolic pathways in depth.

Description

FUNGIpath is a new tool built using a two-stage approach. Groups of orthologous proteins
predicted using complementary methods of detection were collected in a relational
database. Each group was further mapped on to steps in the metabolic pathways published
in the public databases KEGG and MetaCyc. As a result, FUNGIpath allows the primary
and secondary metabolisms of the different fungal species represented in the database
to be compared easily, making it possible to assess the level of specificity of various
pathways at different taxonomic distances. It is freely accessible at http://www.fungipath.u-psud.frwebcite.

Conclusions

As more and more fungal genomes are expected to be sequenced during the coming years,
FUNGIpath should help progressively to reconstruct the ancestral primary and secondary
metabolisms of the main branches of the fungal tree of life and to elucidate the evolution
of these ancestral fungal metabolisms to various specific derived metabolisms.